The present methods and kits relate broadly to the identification of organisms using nucleic acid amplification techniques. In particular, the methods and kits relate to distinguishing closely related species or subspecies of microorganisms.
In clinical settings, it is often useful to be able to distinguish pathogens from closely related species or subspecies. For example, Neisseria gonorrhoeae is recognized as one of the most prevalent sexually transmitted bacteria in the world. Accurate diagnosis of this bacterial infection is critical for preventing serious consequences of long-term infections. Unfortunately, screening efforts in low-prevalence populations coupled with the genomic similarity of many non-gonococcal Neisseria species can potentially lead to the generation of false-positive results using amplified detection techniques such as the polymerase chain reaction (PCR). Although the treatment of such infections is relatively safe and inexpensive, the psychosocial implications of false-positive results can be detrimental to the patients involved. Accordingly, new tests for Neisseria gonorrhoeae capable of discriminating between N. gonorrhoeae and other genomically similar non-gonococcal Neisseria species are highly desirable. More generally, there is a need in the art for methods that can distinguish among closely related species or subspecies of microorganisms, especially in a clinical setting.